PDBsum entry 1upn

Virus/receptor

PDB id: 1upn

Contents

Protein chains

289 a.a. *

252 a.a. *

238 a.a. *

60 a.a. *

125 a.a. *

* Residue conservation analysis

PDB id:

1upn

Name:

Virus/receptor

Title:

Complex of echovirus type 12 with domains 3 and 4 of its receptor decay accelerating factor (cd55) by cryo electron microscopy at 16 a

Structure:

Echovirus 11 coat protein vp1. Chain: a. Echovirus 11 coat protein vp2. Chain: b. Echovirus 11 coat protein vp3. Chain: c. Echovirus 11 coat protein vp4. Chain: d. Other_details: structure of echovirus type 11 fitted into cryo-em

Source:

Human echovirus 11. Organism_taxid: 12078. Strain: gregory. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

Authors:

D.Bhella,I.G.Goodfellow,P.Roversi,D.Pettigrew,Y.Chaudry,D.J.Evans, S.M.Lea

Key ref:

D.Bhella et al. (2004). The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55). J Biol Chem, 279, 8325-8332. PubMed id: 14634014 DOI: 10.1074/jbc.M311334200

Date:

08-Oct-03 Release date: 07-Jan-04

Protein chain

Q8JKE8  (Q8JKE8_9ENTO) -  Genome polyprotein from Echovirus E11

Seq: 2195 a.a.

Struc: 289 a.a.

Protein chain

Q8JKE8  (Q8JKE8_9ENTO) -  Genome polyprotein from Echovirus E11

Seq: 2195 a.a.

Struc: 252 a.a.*

Protein chain

Q8JKE8  (Q8JKE8_9ENTO) -  Genome polyprotein from Echovirus E11

Seq: 2195 a.a.

Struc: 238 a.a.*

Protein chain

Q8JKE8  (Q8JKE8_9ENTO) -  Genome polyprotein from Echovirus E11

Seq: 2195 a.a.

Struc: 60 a.a.

Protein chain

P08174  (DAF_HUMAN) -  Complement decay-accelerating factor from Homo sapiens

Seq: 381 a.a.

Struc: 125 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: Chains A, B, C, D: E.C.3.4.22.28 - picornain 3C.
• Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 3: Chains A, B, C, D: E.C.3.4.22.29 - picornain 2A.
• Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 4: Chains A, B, C, D: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M311334200

J Biol Chem 279:8325-8332 (2004)

PubMed id: 14634014

The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).

D.Bhella, I.G.Goodfellow, P.Roversi, D.Pettigrew, Y.Chaudhry, D.J.Evans, S.M.Lea.

ABSTRACT

Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses.

Selected figure(s)

Figure 2.
FIG. 2. Stereo pairs of surface rendered three-dimensional reconstructions of unlabeled EV12 virions (A) and DAF[34]-labeled virions (B). Isosurfaces of these reconstructions are merged and rendered in their respective color schemes to highlight the differences in density attributed to the two SCR domain fragment of DAF (C). A low resolution representation of EV7 bound to DAF[1234], derived from PDB code 1M11 [PDB] (30), highlights the differently oriented densities in these two complexes (D). In this model the densities of two copies of DAF[1234] are superimposed, laying across the virion 2-fold symmetry axes, giving rise to a hybrid density representing the two possible positions for the molecule. A radial depth-cue color scheme is used to indicate distance from the center of the virion (see the key).

Figure 5.
FIG. 5. A comparison of the low resolution three-dimensional reconstruction of EV12-DAF[34] (A) and a space-filling representation of the EV12-DAF[34] complex (B), generated using the crystallographic co-ordinates for EV11 and DAF[34]. Radial depth-cueing emphasizes the distance between atoms or regions of density and the center of the virion such that dark colors are close to the center and light colors are farther away. EV12 (and EV11) is colored in shades of blue, whereas DAF[34] is colored in green. A space-filling representation of the EV7-DAF[1234] complex (30) (C) highlights the different orientation of DAF bound to these two viruses. The model deposited under PDB code 1M11 [PDB] contains -carbon atoms only; this view is therefore rendered with the atomic radii for each atom set to 3.5Å. EV7 is colored in shades of purple, and the receptor is in red. A close-up view of DAF[34] shown as in panel B but rotated 180^o about a vertical axis exposes the residues buried in the virus-receptor complex (D). Residues are colored according to their contribution to the total contact area ( 840 Å2); yellow (1 < 5%), orange (5 < 9%), and red (9%+). A close-up view of EV11 without the receptor in place exposes buried residues on the surface of the capsid that are colored according to the same scheme (E); the biological protomer is indicated.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 8325-8332) copyright 2004.

Figures were selected by the author.